>>43109619worded the last one wrong
In the strange ending for "The Giant Woman!" (if you're male), then the MC cries out that his girlfriend is in the pokeball. River will then say "It's touching that you can treasure a Pokemon as much as you would a girlfriend."
Of course with the female protag it's the exact same line but with girlfriend swapped out for sister, so it's not really an explicit implication that he sees the Pokemon as your girlfriend but it's one conclusion you can come to.